1
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Kienlein M, Zacharias M, Reif MM. Efficient and accurate calculation of proline cis/trans isomerization free energies from Hamiltonian replica exchange molecular dynamics simulations. Structure 2023; 31:1473-1484.e6. [PMID: 37657438 DOI: 10.1016/j.str.2023.08.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 04/17/2023] [Accepted: 08/07/2023] [Indexed: 09/03/2023]
Abstract
Proline cis/trans isomerization plays an important role in many biological processes but occurs on time scales not accessible to brute-force molecular dynamics (MD) simulations. We have designed a new Hamiltonian replica exchange scheme, ω-bias potential replica exchange molecular dynamics (ωBP-REMD), to efficiently and accurately calculate proline cis/trans isomerization free energies. ωBP-REMD is applied to various proline-containing tripeptides and a biologically important proline residue in the N2-domain of the gene-3-protein of phage fd in the wildtype and mutant variants of the protein. Excellent cis/trans transition rates are obtained. Reweighting of the sampled probability distribution along the peptide bond dihedral angle allows construction of the corresponding free-energy profile and calculation of the cis/trans isomerization free energy with high statistical precision. Very good agreement with experimental data is obtained. ωBP-REMD outperforms standard umbrella sampling in terms of convergence and agreement with experiment and strongly reduces perturbation of the local structure near the proline residue.
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Affiliation(s)
- Maximilian Kienlein
- Center for Functional Protein Assemblies (CPA), Physics Department, Chair of Theoretical Biophysics (T38), Technical University of Munich, Ernst-Otto-Fischer-Str. 8, 85748 Garching, Germany
| | - Martin Zacharias
- Center for Functional Protein Assemblies (CPA), Physics Department, Chair of Theoretical Biophysics (T38), Technical University of Munich, Ernst-Otto-Fischer-Str. 8, 85748 Garching, Germany
| | - Maria M Reif
- Center for Functional Protein Assemblies (CPA), Physics Department, Chair of Theoretical Biophysics (T38), Technical University of Munich, Ernst-Otto-Fischer-Str. 8, 85748 Garching, Germany.
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2
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Malquin N, Rahgoshay K, Lensen N, Chaume G, Miclet E, Brigaud T. CF 2H as a hydrogen bond donor group for the fine tuning of peptide bond geometry with difluoromethylated pseudoprolines. Chem Commun (Camb) 2019; 55:12487-12490. [PMID: 31566647 DOI: 10.1039/c9cc05771d] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
CF2H-Pseudoprolines obtained from difluoroacetaldehyde hemiacetal and serine are stable proline surrogates. The consequence of the incorporation of the CF2H group is an important decrease of the trans to cis amide bond isomerization energy and a remarkable stabilisation of the cis conformer by an hydrogen bond.
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Affiliation(s)
- N Malquin
- Laboratory of Chemical Biology (LCB, EA 4505), Université de Cergy-Pontoise, 5 Mail Gay-Lussac, 95000 Cergy-Pontoise, France.
| | - K Rahgoshay
- Laboratory of Chemical Biology (LCB, EA 4505), Université de Cergy-Pontoise, 5 Mail Gay-Lussac, 95000 Cergy-Pontoise, France.
| | - N Lensen
- Laboratory of Chemical Biology (LCB, EA 4505), Université de Cergy-Pontoise, 5 Mail Gay-Lussac, 95000 Cergy-Pontoise, France.
| | - G Chaume
- Laboratory of Chemical Biology (LCB, EA 4505), Université de Cergy-Pontoise, 5 Mail Gay-Lussac, 95000 Cergy-Pontoise, France.
| | - E Miclet
- Sorbonne Université, École Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, 75005 Paris, France
| | - T Brigaud
- Laboratory of Chemical Biology (LCB, EA 4505), Université de Cergy-Pontoise, 5 Mail Gay-Lussac, 95000 Cergy-Pontoise, France.
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3
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Hasanbašić S, Taler-Verčič A, Puizdar V, Stoka V, Tušek Žnidarič M, Vilfan A, Berbić S, Žerovnik E. Prolines Affect the Nucleation Phase of Amyloid Fibrillation Reaction; Mutational Analysis of Human Stefin B. ACS Chem Neurosci 2019; 10:2730-2740. [PMID: 30924329 PMCID: PMC6727212 DOI: 10.1021/acschemneuro.8b00621] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
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Proline
residues play a prominent role in protein folding and aggregation.
We investigated the influence of single prolines and their combination
on oligomerization and the amyloid fibrillation reaction of human
stefin B (stB). The proline mutants influenced the distribution of
oligomers between monomers, dimers, and tetramers as shown by the
size-exclusion chromatography. Only P74S showed higher oligomers,
reminiscent of the molten globule reported previously for the P74S
of stB-Y31 variant. The proline mutants also inhibited to various
degree the amyloid fibrillation reaction. At 30 and 37 °C, inhibition
was complete for the P74S single mutant, two double mutants (P6L P74S
and P74S P79S), and for the triple mutant P6L P11S P74S. At 30 °C
the single mutant P6L completely inhibited the reaction, while P11S
and P79S formed amyloid fibrils with a prolonged lag phase. P36D did
not show a lag phase, reminiscent of a downhill polymerization model.
At 37 °C in addition to P36D, P11S, and P79S, P6L and P11S P74S
also started to fibrillate; however, the yield of the fibrils was
much lower than that of the wild-type protein as judged by transmission
electron microscopy. Thus, Pro 74 cis/trans isomerization
proves to be the key event, acting as a switch toward an amyloid transition.
Using our previous model of nucleation and growth, we simulated the
kinetics of all the mutants that exhibited sigmoidal fibrillation
curves. To our surprise, the nucleation phase was most affected by
Pro cis/trans isomerism, rather than the fibril elongation
phase.
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Affiliation(s)
- Samra Hasanbašić
- Jožef Stefan International Postgraduate School, Jamova 39, 1000 Ljubljana, Slovenia
- Faculty of Pharmacy, Department of Biochemistry, University of Tuzla, Univerzitetska 1, 75000 Tuzla, Bosnia and Herzegovina
| | - Ajda Taler-Verčič
- Center of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova 39, 1000 Ljubljana, Slovenia
| | | | - Veronika Stoka
- Jožef Stefan International Postgraduate School, Jamova 39, 1000 Ljubljana, Slovenia
| | - Magda Tušek Žnidarič
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | | | - Selma Berbić
- Faculty of Pharmacy, Department of Biochemistry, University of Tuzla, Univerzitetska 1, 75000 Tuzla, Bosnia and Herzegovina
| | - Eva Žerovnik
- Jožef Stefan International Postgraduate School, Jamova 39, 1000 Ljubljana, Slovenia
- Center of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Jamova 39, 1000 Ljubljana, Slovenia
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4
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Levterov VV, Michurin O, Borysko PO, Zozulya S, Sadkova IV, Tolmachev AA, Mykhailiuk PK. Photochemical In-Flow Synthesis of 2,4-Methanopyrrolidines: Pyrrolidine Analogues with Improved Water Solubility and Reduced Lipophilicity. J Org Chem 2018; 83:14350-14361. [PMID: 30358395 DOI: 10.1021/acs.joc.8b02071] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A practical synthesis of 2,4-methanopyrrolidines was elaborated. The key synthetic step was an intramolecular photochemical [2 + 2]-cycloaddition of an acrylic acid derivative in flow. In spite of a higher molecular weight, 2,4-methanopyrrolidines were shown to have higher solubility in water and lower lipophilicity than pyrrolidines, important characteristics of bioactive molecules in drug design.
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Affiliation(s)
- Vadym V Levterov
- Enamine, Ltd. , Chervonotkatska 78 , Kyiv 02094 , Ukraine (www.enamine.net)
| | - Oleg Michurin
- Enamine, Ltd. , Chervonotkatska 78 , Kyiv 02094 , Ukraine (www.enamine.net)
| | - Petro O Borysko
- Bienta, Chervonotkatska 78 , Kyiv 02094 , Ukraine (www.bienta.net)
| | - Sergey Zozulya
- Bienta, Chervonotkatska 78 , Kyiv 02094 , Ukraine (www.bienta.net)
| | - Iryna V Sadkova
- Enamine, Ltd. , Chervonotkatska 78 , Kyiv 02094 , Ukraine (www.enamine.net)
| | - Andrey A Tolmachev
- Enamine, Ltd. , Chervonotkatska 78 , Kyiv 02094 , Ukraine (www.enamine.net).,Department of Chemistry , Taras Shevchenko National University of Kyiv , Volodymyrska 64 , Kyiv 01601 , Ukraine (www.mykhailiukchem.org)
| | - Pavel K Mykhailiuk
- Enamine, Ltd. , Chervonotkatska 78 , Kyiv 02094 , Ukraine (www.enamine.net).,Department of Chemistry , Taras Shevchenko National University of Kyiv , Volodymyrska 64 , Kyiv 01601 , Ukraine (www.mykhailiukchem.org)
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5
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Matena A, Rehic E, Hönig D, Kamba B, Bayer P. Structure and function of the human parvulins Pin1 and Par14/17. Biol Chem 2018; 399:101-125. [PMID: 29040060 DOI: 10.1515/hsz-2017-0137] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 09/29/2017] [Indexed: 12/16/2022]
Abstract
Parvulins belong to the family of peptidyl-prolyl cis/trans isomerases (PPIases) assisting in protein folding and in regulating the function of a broad variety of proteins in all branches of life. The human representatives Pin1 and Par14/17 are directly involved in processes influencing cellular maintenance and cell fate decisions such as cell-cycle progression, metabolic pathways and ribosome biogenesis. This review on human parvulins summarizes the current knowledge of these enzymes and intends to oppose the well-studied Pin1 to its less well-examined homolog human Par14/17 with respect to structure, catalytic and cellular function.
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Affiliation(s)
- Anja Matena
- Structural and Medicinal Biochemistry, Center for Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, D-45117 Essen, Germany
| | - Edisa Rehic
- Structural and Medicinal Biochemistry, Center for Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, D-45117 Essen, Germany
| | - Dana Hönig
- Structural and Medicinal Biochemistry, Center for Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, D-45117 Essen, Germany
| | - Bianca Kamba
- Structural and Medicinal Biochemistry, Center for Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, D-45117 Essen, Germany
| | - Peter Bayer
- Structural and Medicinal Biochemistry, Center for Medical Biotechnology (ZMB), Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 2, D-45117 Essen, Germany
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6
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Baliga C, Varadarajan R, Aghera N. Homodimeric Escherichia coli Toxin CcdB (Controller of Cell Division or Death B Protein) Folds via Parallel Pathways. Biochemistry 2016; 55:6019-6031. [PMID: 27696818 DOI: 10.1021/acs.biochem.6b00726] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The existence of parallel pathways in the folding of proteins seems intuitive, yet remains controversial. We explore the folding kinetics of the homodimeric Escherichia coli toxin CcdB (Controller of Cell Division or Death B protein) using multiple optical probes and approaches. Kinetic studies performed as a function of protein and denaturant concentrations demonstrate that the folding of CcdB is a four-state process. The two intermediates populated during folding are present on parallel pathways. Both form by rapid association of the monomers in a diffusion limited manner and appear to be largely unstructured, as they are silent to the optical probes employed in the current study. The existence of parallel pathways is supported by the insensitivity of the amplitudes of the refolding kinetic phases to the different probes used in the study. More importantly, interrupted refolding studies and ligand binding studies clearly demonstrate that the native state forms in a biexponential manner, implying the presence of at least two pathways. Our studies indicate that the CcdA antitoxin binds only to the folded CcdB dimer and not to any earlier folding intermediates. Thus, despite being part of the same operon, the antitoxin does not appear to modulate the folding pathway of the toxin encoded by the downstream cistron. This study highlights the utility of ligand binding in distinguishing between sequential and parallel pathways in protein folding studies, while also providing insights into molecular interactions during folding in Type II toxin-antitoxin systems.
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Affiliation(s)
- Chetana Baliga
- Molecular Biophysics Unit, Indian Institute of Science , Bangalore 560 012, India
| | - Raghavan Varadarajan
- Molecular Biophysics Unit, Indian Institute of Science , Bangalore 560 012, India.,Jawaharlal Nehru Centre for Advanced Scientific Research , Jakkur P.O., Bangalore 560 004, India
| | - Nilesh Aghera
- Molecular Biophysics Unit, Indian Institute of Science , Bangalore 560 012, India
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7
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A comparative study between the electro-activation technique and conventional extraction method on the extractability, composition and physicochemical properties of canola protein concentrates and isolates. FOOD BIOSCI 2015. [DOI: 10.1016/j.fbio.2015.04.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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8
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Talei D, Valdiani A, Maziah M, Sagineedu SR, Abiri R. Salt stress-induced protein pattern associated with photosynthetic parameters and andrographolide content in Andrographis paniculata Nees. Biosci Biotechnol Biochem 2015; 79:51-8. [DOI: 10.1080/09168451.2014.963499] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Abstract
Andrographis paniculata is a multifunctional medicinal plant and a potent source of bioactive compounds. Impact of environmental stresses such as salinity on protein diversification, as well as the consequent changes in the photosynthetic parameters and andrographolide content (AG) of the herb, has not yet been thoroughly investigated. The present study showed that the salinity affects the protein pattern, and subsequently, it decreased the photosynthetic parameters, protein content, total dry weight, and total crude extract. Exceptionally, the AG content was increased (p ≤ 0.01). Moreover, it was noticed that the salinity at 12 dS m−1 led to the maximum increase in AG content in all accessions. Interestingly, the leaf protein analysis revealed that the two polymorphic protein bands as low- and medium-sized of 17 and 45 kDa acted as the activator agents for the photosynthetic parameters and AG content. Protein sequencing and proteomic analysis can be conducted based on the present findings in the future.
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Affiliation(s)
- Daryush Talei
- Medicinal Plants Research Center, Shahed University, Tehran, Iran
- Faculty of Biotechnology and Biomolecular Sciences, Department of Cell and Molecular Biology, Universiti Putra Malaysia, Serdang, Malaysia
| | - Alireza Valdiani
- Faculty of Biotechnology and Biomolecular Sciences, Department of Biochemistry, Universiti Putra Malaysia, Serdang, Malaysia
| | - Mahmood Maziah
- Faculty of Biotechnology and Biomolecular Sciences, Department of Biochemistry, Universiti Putra Malaysia, Serdang, Malaysia
- Institute of Tropical Agriculture, Universiti Putra Malaysia, Serdang, Malaysia
- Institute of Bioscience, Universiti Putra Malaysia, Serdang, Malaysia
| | - Sreenivasa Rao Sagineedu
- Department of Pharmaceutical Chemistry, School of Pharmacy, International Medical University, Kuala Lumpur, Malaysia
| | - Rambod Abiri
- Faculty of Biotechnology and Biomolecular Sciences, Department of Biochemistry, Universiti Putra Malaysia, Serdang, Malaysia
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9
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Chaume G, Simon J, Caupène C, Lensen N, Miclet E, Brigaud T. Incorporation of CF3–Pseudoprolines into Peptides: A Methodological Study. J Org Chem 2013; 78:10144-53. [DOI: 10.1021/jo401494q] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Grégory Chaume
- Laboratoire SOSCO, Université de Cergy-Pontoise, EA 4505, 5 Mail Gay-Lussac, 95000 Cergy-Pontoise, France
| | - Julien Simon
- Laboratoire SOSCO, Université de Cergy-Pontoise, EA 4505, 5 Mail Gay-Lussac, 95000 Cergy-Pontoise, France
| | - Caroline Caupène
- Laboratoire SOSCO, Université de Cergy-Pontoise, EA 4505, 5 Mail Gay-Lussac, 95000 Cergy-Pontoise, France
| | - Nathalie Lensen
- Laboratoire SOSCO, Université de Cergy-Pontoise, EA 4505, 5 Mail Gay-Lussac, 95000 Cergy-Pontoise, France
| | - Emeric Miclet
- Laboratoire des
BioMolécules, UMR 7203, Ecole Normale Supérieure, UPMC Paris 06, 4 Place Jussieu, 75005 Paris, France
| | - Thierry Brigaud
- Laboratoire SOSCO, Université de Cergy-Pontoise, EA 4505, 5 Mail Gay-Lussac, 95000 Cergy-Pontoise, France
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10
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Chen J, Edwards SA, Gräter F, Baldauf C. On the cis to trans isomerization of prolyl-peptide bonds under tension. J Phys Chem B 2012; 116:9346-51. [PMID: 22770126 DOI: 10.1021/jp3042846] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The cis peptide bond is a characteristic feature of turns in protein structures and can play the role of a hinge in protein folding. Such cis conformations are most commonly found at peptide bonds immediately preceding proline residues, as the cis and trans states for such bonds are close in energy. However, isomerization over the high rotational barrier is slow. In this study, we investigate how mechanical force accelerates the cis to trans isomerization of the prolyl-peptide bond in a stretched backbone. We employ hybrid quantum mechanical/molecular mechanical force-clamp molecular dynamics simulations in order to describe the electronic effects involved. Under tension, the bond order of the prolyl-peptide bond decreases from a partially double toward a single bond, involving a reduction in the electronic conjugation around the peptide bond. The conformational change from cis to extended trans takes place within a few femtoseconds through a nonplanar state of the nitrogen of the peptide moiety in the transition state region, whereupon the partial double-bond character and planarity of the peptide bond in the final trans state is restored. Our findings give insight into how prolyl-peptide bonds might act as force-modulated mechanical timers or switches in the refolding of proteins.
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Affiliation(s)
- Jian Chen
- CAS-MPG Partner Institute and Key Laboratory for Computational Biology (PICB), 320 Yue Yang Road, Shanghai 200031, China
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11
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Tkachenko AN, Radchenko DS, Mykhailiuk PK, Grygorenko OO, Komarov IV. 4-Fluoro-2,4-methanoproline. Org Lett 2009; 11:5674-6. [DOI: 10.1021/ol902381w] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Anton N. Tkachenko
- Department of Chemistry, Kyiv National Taras Shevchenko University, Vul. Volodymyrska 64, 01033 Kyiv, Ukraine, and Enamine Ltd., Vul. Oleksandra Matrosova 23, 01103 Kyiv, Ukraine
| | - Dmytro S. Radchenko
- Department of Chemistry, Kyiv National Taras Shevchenko University, Vul. Volodymyrska 64, 01033 Kyiv, Ukraine, and Enamine Ltd., Vul. Oleksandra Matrosova 23, 01103 Kyiv, Ukraine
| | - Pavel K. Mykhailiuk
- Department of Chemistry, Kyiv National Taras Shevchenko University, Vul. Volodymyrska 64, 01033 Kyiv, Ukraine, and Enamine Ltd., Vul. Oleksandra Matrosova 23, 01103 Kyiv, Ukraine
| | - Oleksandr O. Grygorenko
- Department of Chemistry, Kyiv National Taras Shevchenko University, Vul. Volodymyrska 64, 01033 Kyiv, Ukraine, and Enamine Ltd., Vul. Oleksandra Matrosova 23, 01103 Kyiv, Ukraine
| | - Igor V. Komarov
- Department of Chemistry, Kyiv National Taras Shevchenko University, Vul. Volodymyrska 64, 01033 Kyiv, Ukraine, and Enamine Ltd., Vul. Oleksandra Matrosova 23, 01103 Kyiv, Ukraine
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12
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Zandi M, Mirzadeh H, Mayer C. Early stages of gelation in gelatin solution detected by dynamic oscillating rheology and nuclear magnetic spectroscopy. Eur Polym J 2007. [DOI: 10.1016/j.eurpolymj.2007.01.011] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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